Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: 7GLYK

Calculation Name: 3RIU-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3RIU

Chain ID: C

ChEMBL ID:

UniProt ID: Q9VF77

Base Structure: X-ray

Registration Date: 2023-06-20

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptHSide
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 207
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2476773.136865
FMO2-HF: Nuclear repulsion 2389606.020941
FMO2-HF: Total energy -87167.115924
FMO2-MP2: Total energy -87417.949642


3D Structure
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
ligand interaction
Ligand binding energy
"
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
N/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(C:31:VAL)


Summations of interaction energy for fragment #1(C:31:VAL)
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
-3.859-1.4423.852-1.874-4.3940.007
Interaction energy analysis for fragmet #1(C:31:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.036 / q_NPA : 0.003
Distance from base fragment(s) [Å]
Dist
Interaction energy by IFIE and PIEDA
[kcal/mol]
| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >
Fragment charge [e]
FCHARGE q_Mulliken
q_NPA q(I=>J)
Residue
Res #    RES   
Sort
Graph Options
X Axis Label
Y Axis Max Y Axis Min
Display   
frag_NumFragment number. ChainChain species. Res #Residue number. RES3-letter code of amino acid residue, ligand and solvent molecule. FCHARGEFormal charge [e]. q_MullikenFragment charge evaluated by Mulliken charge [e]. q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e]. DISTDistance from Ligand [Å]. TotalIFIE at MP2 level [kcal/mol]. ESElectro static interaction energy by PIEDA [kcal/mol]. EXExchange-repulsion energy by PIEDA [kcal/mol]. CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol]. DI(MP2)Dispersion energy by PIEDA [kcal/mol]. q(I=>J)Charge transfer value from I to J fragmens [e].
3C33GLN00.0510.0322.103-2.285-0.3253.815-1.990-3.7840.007
4C34PHE00.0500.0083.430-1.342-0.8850.0370.116-0.6100.000
5C35ARG10.9410.9845.900-0.135-0.1350.0000.0000.0000.000
6C36ILE00.003-0.0067.309-0.108-0.1080.0000.0000.0000.000
7C37TYR00.0600.0366.4880.0960.0960.0000.0000.0000.000
8C38SER00.0260.0109.437-0.147-0.1470.0000.0000.0000.000
9C39ASN00.003-0.01011.322-0.080-0.0800.0000.0000.0000.000
10C40GLU-1-0.926-0.95312.1860.5690.5690.0000.0000.0000.000
11C41LEU0-0.043-0.02512.482-0.034-0.0340.0000.0000.0000.000
12C42ILE00.0270.03114.453-0.040-0.0400.0000.0000.0000.000
13C43MET0-0.025-0.01417.220-0.018-0.0180.0000.0000.0000.000
14C44LYS10.8760.92418.110-0.241-0.2410.0000.0000.0000.000
15C45HIS0-0.009-0.01016.466-0.027-0.0270.0000.0000.0000.000
16C46ASP-1-0.814-0.88821.2490.0420.0420.0000.0000.0000.000
17C47ARG10.8360.90723.423-0.124-0.1240.0000.0000.0000.000
18C48HIS00.0340.01524.465-0.001-0.0010.0000.0000.0000.000
19C49GLU-1-0.813-0.88125.5400.0240.0240.0000.0000.0000.000
20C50ARG10.8360.89625.045-0.075-0.0750.0000.0000.0000.000
21C51ILE00.0270.01628.535-0.005-0.0050.0000.0000.0000.000
22C52VAL00.0090.00729.577-0.005-0.0050.0000.0000.0000.000
23C53LYS10.8040.91031.644-0.031-0.0310.0000.0000.0000.000
24C54LEU00.0070.00533.644-0.003-0.0030.0000.0000.0000.000
25C55SER0-0.007-0.00534.666-0.003-0.0030.0000.0000.0000.000
26C56ARG10.8370.89230.920-0.029-0.0290.0000.0000.0000.000
27C57ASP-1-0.875-0.95437.6710.0240.0240.0000.0000.0000.000
28C58ILE00.0120.01338.428-0.002-0.0020.0000.0000.0000.000
29C59THR0-0.003-0.01239.744-0.001-0.0010.0000.0000.0000.000
30C60ILE0-0.043-0.02440.812-0.002-0.0020.0000.0000.0000.000
31C61GLU-1-0.889-0.93643.4170.0220.0220.0000.0000.0000.000
32C62SER00.0480.02144.853-0.001-0.0010.0000.0000.0000.000
33C63LYS10.8530.92744.047-0.024-0.0240.0000.0000.0000.000
34C64ARG10.9110.94246.360-0.016-0.0160.0000.0000.0000.000
35C65ILE0-0.027-0.00448.949-0.001-0.0010.0000.0000.0000.000
36C66ILE00.0440.03249.099-0.001-0.0010.0000.0000.0000.000
37C67PHE0-0.023-0.01950.775-0.001-0.0010.0000.0000.0000.000
38C68LEU0-0.078-0.01753.652-0.001-0.0010.0000.0000.0000.000
39C69LEU0-0.042-0.01554.240-0.001-0.0010.0000.0000.0000.000
40C70HIS0-0.016-0.02053.102-0.001-0.0010.0000.0000.0000.000
41C71SER0-0.109-0.04958.063-0.001-0.0010.0000.0000.0000.000
42C72ILE0-0.004-0.00160.987-0.001-0.0010.0000.0000.0000.000
43C73ASP-1-0.767-0.85861.9510.0110.0110.0000.0000.0000.000
44C74SER0-0.103-0.08165.1880.0010.0010.0000.0000.0000.000
45C75ARG10.7730.87168.294-0.009-0.0090.0000.0000.0000.000
46C76LYS10.9660.99070.220-0.009-0.0090.0000.0000.0000.000
47C77GLN0-0.048-0.05369.7480.0000.0000.0000.0000.0000.000
48C78ASN0-0.0540.00065.239-0.001-0.0010.0000.0000.0000.000
49C79LYS10.9820.98167.103-0.010-0.0100.0000.0000.0000.000
50C80GLU-1-0.843-0.92064.2970.0140.0140.0000.0000.0000.000
51C81LYS10.8830.92759.487-0.014-0.0140.0000.0000.0000.000
52C82VAL0-0.022-0.02759.1640.0010.0010.0000.0000.0000.000
53C83LEU00.0950.05158.2300.0010.0010.0000.0000.0000.000
54C84GLU-1-0.823-0.90658.2000.0200.0200.0000.0000.0000.000
55C85GLU-1-0.859-0.92955.7190.0170.0170.0000.0000.0000.000
56C86ALA00.0250.01854.6170.0010.0010.0000.0000.0000.000
57C87ARG10.9190.94553.437-0.021-0.0210.0000.0000.0000.000
58C88GLN0-0.026-0.00353.2120.0010.0010.0000.0000.0000.000
59C89ARG10.9080.96150.358-0.017-0.0170.0000.0000.0000.000
60C90LEU00.0340.01548.5950.0010.0010.0000.0000.0000.000
61C91ASN0-0.017-0.03248.3040.0030.0030.0000.0000.0000.000
62C92LYS10.8420.92646.615-0.021-0.0210.0000.0000.0000.000
63C93LEU0-0.043-0.01743.5270.0010.0010.0000.0000.0000.000
64C94ILE00.0510.03343.8340.0020.0020.0000.0000.0000.000
65C95ALA00.0230.00543.3530.0020.0020.0000.0000.0000.000
66C96VAL0-0.059-0.04439.8710.0020.0020.0000.0000.0000.000
67C97ASN00.0470.01439.3190.0050.0050.0000.0000.0000.000
68C98PHE00.0280.01538.5190.0030.0030.0000.0000.0000.000
69C99ARG10.8910.94337.017-0.030-0.0300.0000.0000.0000.000
70C100ALA0-0.054-0.03534.6630.0030.0030.0000.0000.0000.000
71C101VAL00.0560.03734.0310.0040.0040.0000.0000.0000.000
72C102ALA0-0.022-0.00533.6310.0050.0050.0000.0000.0000.000
73C103LEU0-0.110-0.04328.6480.0040.0040.0000.0000.0000.000
74C104GLU-1-0.825-0.90428.7840.1130.1130.0000.0000.0000.000
75C105LEU00.000-0.00626.6760.0010.0010.0000.0000.0000.000
76C106ARG10.7800.85121.631-0.201-0.2010.0000.0000.0000.000
77C107ASP-1-0.833-0.87825.4720.1700.1700.0000.0000.0000.000
78C108GLN0-0.010-0.02628.549-0.002-0.0020.0000.0000.0000.000
79C109ASP-1-0.789-0.88031.4640.0880.0880.0000.0000.0000.000
80C110VAL00.0000.02326.393-0.003-0.0030.0000.0000.0000.000
81C111TYR00.0640.00128.770-0.004-0.0040.0000.0000.0000.000
82C112GLN0-0.0210.00622.2140.0060.0060.0000.0000.0000.000
83C113PHE00.0570.00823.3020.0040.0040.0000.0000.0000.000
84C114ARG10.8540.93028.047-0.098-0.0980.0000.0000.0000.000
85C115SER0-0.0090.00727.686-0.006-0.0060.0000.0000.0000.000
86C116SER00.0530.01230.033-0.006-0.0060.0000.0000.0000.000
87C117TYR0-0.0260.02932.274-0.005-0.0050.0000.0000.0000.000
88C118SER00.045-0.00434.177-0.003-0.0030.0000.0000.0000.000
89C119PRO00.0380.01936.7210.0000.0000.0000.0000.0000.000
90C120GLY00.0370.04138.255-0.001-0.0010.0000.0000.0000.000
91C121LEU0-0.011-0.00638.136-0.001-0.0010.0000.0000.0000.000
92C122GLN0-0.050-0.02839.4460.0010.0010.0000.0000.0000.000
93C123GLU-1-0.761-0.87742.1780.0250.0250.0000.0000.0000.000
94C124PHE0-0.0250.00343.394-0.002-0.0020.0000.0000.0000.000
95C125ILE00.0110.02342.740-0.002-0.0020.0000.0000.0000.000
96C126GLU-1-0.847-0.89346.4470.0240.0240.0000.0000.0000.000
97C127ALA00.022-0.00748.192-0.001-0.0010.0000.0000.0000.000
98C128TYR0-0.030-0.01448.662-0.001-0.0010.0000.0000.0000.000
99C129THR0-0.004-0.02849.713-0.001-0.0010.0000.0000.0000.000
100C130TYR0-0.009-0.01552.246-0.001-0.0010.0000.0000.0000.000
101C131MET0-0.060-0.02853.770-0.001-0.0010.0000.0000.0000.000
102C132GLU-1-0.753-0.88753.7820.0300.0300.0000.0000.0000.000
103C133TYR00.0080.00056.365-0.001-0.0010.0000.0000.0000.000
104C134LEU0-0.020-0.00957.883-0.001-0.0010.0000.0000.0000.000
105C135CYS0-0.108-0.04759.114-0.001-0.0010.0000.0000.0000.000
106C136HIS0-0.078-0.01960.8870.0000.0000.0000.0000.0000.000
107C137GLU-1-0.876-0.92463.2250.0180.0180.0000.0000.0000.000
108C145THR0-0.024-0.02761.5080.0000.0000.0000.0000.0000.000
109C146LYS10.7780.87954.893-0.032-0.0320.0000.0000.0000.000
110C147SER0-0.014-0.00256.9110.0000.0000.0000.0000.0000.000
111C148VAL00.095-0.00354.5090.0000.0000.0000.0000.0000.000
112C149SER0-0.082-0.02950.7390.0010.0010.0000.0000.0000.000
113C150ASP-1-0.830-0.88250.4540.0350.0350.0000.0000.0000.000
114C151TRP00.026-0.00743.8640.0010.0010.0000.0000.0000.000
115C152GLN0-0.0290.00245.5580.0020.0020.0000.0000.0000.000
116C153ALA00.0410.01147.0480.0010.0010.0000.0000.0000.000
117C154ILE0-0.027-0.00744.9510.0000.0000.0000.0000.0000.000
118C155GLN00.0700.03341.6960.0030.0030.0000.0000.0000.000
119C156ALA0-0.044-0.02443.8740.0020.0020.0000.0000.0000.000
120C157VAL0-0.022-0.01046.6350.0000.0000.0000.0000.0000.000
121C158MET0-0.071-0.02741.5910.0000.0000.0000.0000.0000.000
122C159GLN0-0.041-0.02940.7380.0040.0040.0000.0000.0000.000
123C160TYR0-0.026-0.00642.8440.0000.0000.0000.0000.0000.000
124C161VAL0-0.086-0.01838.803-0.002-0.0020.0000.0000.0000.000
125C162GLU-1-0.946-0.95539.7610.0560.0560.0000.0000.0000.000
126C191PHE0-0.032-0.01137.004-0.001-0.0010.0000.0000.0000.000
127C192PHE0-0.024-0.02635.7860.0050.0050.0000.0000.0000.000
128C193VAL00.0050.00935.629-0.002-0.0020.0000.0000.0000.000
129C194ASP-1-0.753-0.87737.9740.0520.0520.0000.0000.0000.000
130C195PRO0-0.015-0.01037.841-0.002-0.0020.0000.0000.0000.000
131C196THR00.009-0.00138.781-0.004-0.0040.0000.0000.0000.000
132C197GLU-1-0.871-0.96036.8220.0620.0620.0000.0000.0000.000
133C198TYR00.014-0.01340.955-0.005-0.0050.0000.0000.0000.000
134C199ILE0-0.0060.00544.177-0.003-0.0030.0000.0000.0000.000
135C200LEU0-0.0590.00140.751-0.003-0.0030.0000.0000.0000.000
136C201GLY00.0920.03244.328-0.003-0.0030.0000.0000.0000.000
137C202LEU00.0480.01545.715-0.002-0.0020.0000.0000.0000.000
138C203SER0-0.057-0.01447.470-0.002-0.0020.0000.0000.0000.000
139C204ASP-1-0.836-0.88145.0850.0310.0310.0000.0000.0000.000
140C205LEU00.0310.04548.539-0.002-0.0020.0000.0000.0000.000
141C206THR0-0.061-0.05551.449-0.002-0.0020.0000.0000.0000.000
142C207GLY0-0.026-0.01851.797-0.002-0.0020.0000.0000.0000.000
143C208GLU-1-0.731-0.88551.8960.0190.0190.0000.0000.0000.000
144C209LEU00.0050.02053.885-0.001-0.0010.0000.0000.0000.000
145C210MET0-0.059-0.03356.133-0.001-0.0010.0000.0000.0000.000
146C211ARG10.7690.87050.050-0.022-0.0220.0000.0000.0000.000
147C212ARG10.9080.94857.343-0.018-0.0180.0000.0000.0000.000
148C213CYS0-0.062-0.02859.931-0.001-0.0010.0000.0000.0000.000
149C214ILE0-0.101-0.04458.799-0.001-0.0010.0000.0000.0000.000
150C215ASN0-0.015-0.00659.0100.0000.0000.0000.0000.0000.000
151C216SER00.0200.02062.639-0.001-0.0010.0000.0000.0000.000
152C217LEU0-0.0250.00366.0830.0000.0000.0000.0000.0000.000
153C218GLY00.017-0.00267.6670.0000.0000.0000.0000.0000.000
154C219SER0-0.027-0.03867.735-0.001-0.0010.0000.0000.0000.000
155C220GLY0-0.030-0.01570.1850.0000.0000.0000.0000.0000.000
156C221ASP-1-0.777-0.85271.7400.0100.0100.0000.0000.0000.000
157C222THR0-0.011-0.03568.6970.0010.0010.0000.0000.0000.000
158C223ASP-1-0.943-0.94670.6820.0120.0120.0000.0000.0000.000
159C224THR00.0230.02966.8960.0000.0000.0000.0000.0000.000
160C225CYS00.0240.01465.3450.0010.0010.0000.0000.0000.000
161C226LEU00.0670.00565.3060.0010.0010.0000.0000.0000.000
162C227ASP-1-0.782-0.89564.5590.0170.0170.0000.0000.0000.000
163C228THR0-0.019-0.00660.3180.0010.0010.0000.0000.0000.000
164C229CYS0-0.094-0.03761.4480.0000.0000.0000.0000.0000.000
165C230LYS10.8860.93862.781-0.018-0.0180.0000.0000.0000.000
166C231ALA00.0340.03159.5740.0010.0010.0000.0000.0000.000
167C232LEU00.003-0.01556.9490.0010.0010.0000.0000.0000.000
168C233GLN0-0.034-0.02258.5130.0010.0010.0000.0000.0000.000
169C234HIS0-0.0210.00259.9330.0000.0000.0000.0000.0000.000
170C235PHE00.0750.03653.3090.0010.0010.0000.0000.0000.000
171C236TYR00.0350.01354.3870.0010.0010.0000.0000.0000.000
172C237SER0-0.028-0.02355.6450.0010.0010.0000.0000.0000.000
173C238GLY0-0.016-0.00655.1730.0010.0010.0000.0000.0000.000
174C239TYR0-0.077-0.08948.3140.0010.0010.0000.0000.0000.000
175C240ILE0-0.111-0.05451.3850.0010.0010.0000.0000.0000.000
176C241SER0-0.0190.00753.5940.0010.0010.0000.0000.0000.000
177C242LEU00.0100.01647.7010.0010.0010.0000.0000.0000.000
178C243ASN00.010-0.00644.932-0.003-0.0030.0000.0000.0000.000
179C244CYS0-0.004-0.00145.6130.0010.0010.0000.0000.0000.000
180C245GLN00.007-0.00844.2420.0010.0010.0000.0000.0000.000
181C246ARG10.8440.93541.867-0.036-0.0360.0000.0000.0000.000
182C247ALA00.0960.07437.536-0.001-0.0010.0000.0000.0000.000
183C248ARG10.8770.90038.800-0.040-0.0400.0000.0000.0000.000
184C249GLU-1-0.832-0.90239.2190.0520.0520.0000.0000.0000.000
185C250LEU00.1380.06441.168-0.002-0.0020.0000.0000.0000.000
186C251TRP00.0360.03244.328-0.002-0.0020.0000.0000.0000.000
187C252ARG10.8970.95238.708-0.041-0.0410.0000.0000.0000.000
188C253LYS10.8550.90644.018-0.035-0.0350.0000.0000.0000.000
189C254ILE00.0500.02147.193-0.002-0.0020.0000.0000.0000.000
190C255THR0-0.036-0.03148.929-0.002-0.0020.0000.0000.0000.000
191C256THR0-0.004-0.00248.925-0.002-0.0020.0000.0000.0000.000
192C257MET00.0120.03850.842-0.001-0.0010.0000.0000.0000.000
193C258LYS10.9580.99753.108-0.022-0.0220.0000.0000.0000.000
194C259GLN00.015-0.00554.8070.0000.0000.0000.0000.0000.000
195C260SER0-0.099-0.06555.048-0.001-0.0010.0000.0000.0000.000
196C261VAL00.0480.01556.962-0.001-0.0010.0000.0000.0000.000
197C262LEU00.0250.01459.262-0.001-0.0010.0000.0000.0000.000
198C263LYS10.8960.95955.289-0.017-0.0170.0000.0000.0000.000
199C264ALA00.0650.02560.938-0.001-0.0010.0000.0000.0000.000
200C265GLU-1-0.852-0.91962.7490.0170.0170.0000.0000.0000.000
201C266ASN0-0.042-0.02264.640-0.001-0.0010.0000.0000.0000.000
202C267VAL00.0390.01564.337-0.001-0.0010.0000.0000.0000.000
203C269TYR0-0.063-0.01568.7950.0000.0000.0000.0000.0000.000
204C270ASN0-0.032-0.02968.978-0.001-0.0010.0000.0000.0000.000
205C271VAL0-0.030-0.00370.4700.0000.0000.0000.0000.0000.000
206C272LYS10.9360.98673.021-0.012-0.0120.0000.0000.0000.000
207C273VAL0-0.011-0.00275.7240.0000.0000.0000.0000.0000.000